State-of-the-art review of secondary pulmonary infections in patients with COVID-19 pneumonia

Infection. 2021 Aug;49(4):591-605. doi: 10.1007/s15010-021-01602-z. Epub 2021 Mar 11.


Background: The incidence of secondary pulmonary infections is not well described in hospitalized COVID-19 patients. Understanding the incidence of secondary pulmonary infections and the associated bacterial and fungal microorganisms identified can improve patient outcomes.

Objective: This narrative review aims to determine the incidence of secondary bacterial and fungal pulmonary infections in hospitalized COVID-19 patients, and describe the bacterial and fungal microorganisms identified.

Method: We perform a literature search and select articles with confirmed diagnoses of secondary bacterial and fungal pulmonary infections that occur 48 h after admission, using respiratory tract cultures in hospitalized adult COVID-19 patients. We exclude articles involving co-infections defined as infections diagnosed at the time of admission by non-SARS-CoV-2 viruses, bacteria, and fungal microorganisms.

Results: The incidence of secondary pulmonary infections is low at 16% (4.8-42.8%) for bacterial infections and lower for fungal infections at 6.3% (0.9-33.3%) in hospitalized COVID-19 patients. Secondary pulmonary infections are predominantly seen in critically ill hospitalized COVID-19 patients. The most common bacterial microorganisms identified in the respiratory tract cultures are Pseudomonas aeruginosa, Klebsiella species, Staphylococcus aureus, Escherichia coli, and Stenotrophomonas maltophilia. Aspergillus fumigatus is the most common microorganism identified to cause secondary fungal pulmonary infections. Other rare opportunistic infection reported such as PJP is mostly confined to small case series and case reports. The overall time to diagnose secondary bacterial and fungal pulmonary infections is 10 days (2-21 days) from initial hospitalization and 9 days (4-18 days) after ICU admission. The use of antibiotics is high at 60-100% involving the studies included in our review.

Conclusion: The widespread use of empirical antibiotics during the current pandemic may contribute to the development of multidrug-resistant microorganisms, and antimicrobial stewardship programs are required for minimizing and de-escalating antibiotics. Due to the variation in definition across most studies, a large, well-designed study is required to determine the incidence, risk factors, and outcomes of secondary pulmonary infections in hospitalized COVID-19 patients.

Keywords: Bacterial infection; COVID-19; Coronavirus disease 2019; Fungal infection; SARS-CoV-2; Secondary infection; Severe acute respiratory syndrome coronavirus 2; Superimposed infection; Superinfection.

Publication types

  • Review

MeSH terms

  • Anti-Bacterial Agents / therapeutic use
  • Antimicrobial Stewardship
  • COVID-19 / complications*
  • COVID-19 / epidemiology
  • Coinfection / diagnosis
  • Coinfection / drug therapy
  • Coinfection / epidemiology
  • Coinfection / microbiology
  • Drug Resistance, Multiple
  • Humans
  • Incidence
  • Lung Diseases, Fungal / epidemiology*
  • Lung Diseases, Fungal / etiology
  • Lung Diseases, Fungal / microbiology
  • Pneumonia, Bacterial / epidemiology*
  • Pneumonia, Bacterial / etiology
  • Pneumonia, Bacterial / microbiology
  • SARS-CoV-2*
  • Time Factors


  • Anti-Bacterial Agents